May 2012 - galaxy-dev - lists.galaxyproject.org

param.dynamic_options: How can I disable escaping HTML tags?
by Tim te Beek 22 May '12

22 May '12

Hi all, Up until today I was happily using the following to produce the options for a Galaxy tool of mine based on a daily updated remote resource: """ <code file="select_taxa.py"/> ... <param name="genomes" type="select" display="checkboxes" multiple="true" optional="true" force_select="false" label="Choose Genomes" dynamic_options="get_complete_genomes()"> """ The get_complete_genomes() call returns and iterator with tuples of ("Label", "Value", False), which are shown to the user. Previously, any HTML tags I added in "Label" were correctly rendered in the browser. However, since updating Galaxy to the latest distribution this morning, my HTML tags now are escaped which shows the tags to the user rather than changing the rendering. Rendering the HTML tags was crucial to retain readability in a tree with over 2000 options, so I would like to enable it again (disable escaping) in my local installation. How can I disable escaping HTML tags in my param.dynamic_options? Thanks in advance, Tim

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Newbie question, adding a custom perl script
by Ciara Ledero 22 May '12

22 May '12

> > Hi there! > Recently, I modified a Galaxy-intended velvet script so that the user would be able to put in his/her desired output directory ( the original script does not allow this). I just used a text box so as to ask for the output directory path (e.g. /home/galaxy/outputFolder). Then I just let Perl do the rest. Maybe in your case, you could just ask for the input and output directory paths. Then maybe you could just generate a text file that logs the end status of the process (i.e. whether it has been successful or not). This text file would be the one that shows up in your history. Cheers, CL Hi, > > A co-worker has a perl script that takes a directory path, and then > interates over a the file in that directory and processes them into an > output directory. > I want to integrate that into galaxy. I've figured out that I'll need > to create a tool XML conf with the inputs , outputs etc. > > My question is what param type should I use for a directory, in the > input and output ? Or maybe what I'm looking for a is an input, output > type that is a set of file (rather than tying it to a filesystem) > > Sorry for my beginners questions ! > > Thanks > > Mac > >

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Public IP Address
by Madeleine Matias 21 May '12

21 May '12

Hello, I recently launched a new instance about 6 minutes ago using BioCloud Central (https://biocloudcentral.herokuapp.com/launch) but did not receive a Public IP address. I'm not sure if the instance was fully launched. Here is the Instance and Image ID I received: Instance ID i-6789fa01 Image ID (AMI) ami-500cd139 Can you please verify if an instance is in fact running and what the Public IP address is? Thank you, Madeleine

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[Errno 32] Broken pipe on uploading file
by xxtdqxx＠gmail.com 21 May '12

21 May '12

Dear Galaxy Team. I installed Galaxy on company server for integrating with our services. And I found some problem in uploading files via API. I tried to upload file from local folder and it works well. But, then I tried to upload file from remote server it throws next exception: 194.226.177.176 - - [21/May/2012:12:38:51 +0200] "POST /api/user/adm/upload?key=71edcbdb2b91c9b2c1125775804d2093 HT TP/1.1" 500 - "-" "Python-urllib/2.6" Debug at: http://cogangs.biobase.de:82/_debug/view/1337592259 ---------------------------------------- Exception happened during processing of request from ('194.226.177.176', 29682) Traceback (most recent call last): File "/data/dat0/galaxy-dist-back/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in _thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 322, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 618, in __init__ self.finish() File "/usr/lib/python2.6/SocketServer.py", line 661, in finish self.wfile.flush() File "/usr/lib/python2.6/socket.py", line 297, in flush self._sock.sendall(buffer(data, write_offset, buffer_size)) error: [Errno 32] Broken pipe ---------------------------------------- Browsing libraries from remote server works well. Please help me to resolve this problem. In attach: archive with debug message, controller class for processing uploading, buidapp.py, wsgi config file and script for request upload file. Server A contains: uploading file, upload_file.py and Galaxy api Server B contains: Galaxy service, upload.py, buildapp.py, wsgi config file Best regards, Nikolay

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How can I connect to galaxy with multiple handlers and Galaxy performances
by julie dubois 21 May '12

21 May '12

Hi, I've follow the instruction of this wiki : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… And when I ran the command : GALAXY_RUN_ALL=1 sh run.sh --daemon I've just obtain this answer in the terminal : Entering daemon mode without this type of line : Handling web0 with log file web0.log First : is it normal and is my apache configuration right : In my Default file I add <Proxy balancer://galaxy>... after my rewrite rules and it replace the instructions :<Proxy http://localhost:8080>... Second : how can I connect in my browser to Galaxy, because I've tried http://localhost:8080/galaxy and http://localhost:8079/galaxy and it didn't work, the browser says me : unable to connect I set this configuration because I want to increase the performances of Galaxy. in fact when I upload a file, with your web server, it run in 20 minutes and with my server it don't finish after 1 hour! Is it normal? Thank you for your attention. julie

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server problem
by L.Y.E. Wong 21 May '12

21 May '12

Dear Galaxy-support, I could not use Galaxy nearly for 2 days, I think there is a problem with the server. If I 'intersect' data sets then it just turned to 'job is wating to run' and never moved on. I have already informed other people working in another city, and they also have the same server problem. I live in the Netherlands (I don't know if you need this info). Could you please give me some information about this problem and how long it will take? Thank you in advance. Kind regards, Elaine Wong De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Academisch Medisch Centrum is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Amsterdam onder nr. 34362777. De Algemene Inkoop Voorwaarden van het AMC zijn van toepassing op en maken integraal onderdeel uit van alle rechtsbetrekkingen, daaronder mede verstaan alle inkoop opdrachten en overeenkomsten, tussen AMC en derden. Deze voorwaarden zijn te raadplegen op www.amc.nl en worden op verzoek toegezonden. ________________________________ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. Academic Medical Center is a legal person by public law and is registered at the Chamber of Commerce for Amsterdam under no. 34362777. The AMC General Purchase Terms constitute an integral part of all legal relations, including but not limited to all purchase orders and contracts, between the AMC and third parties. These terms can be downloaded at the website www.amc.nl and will be sent to you at your request.

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About workflow creation
by Ciara Ledero 21 May '12

21 May '12

Hi all, I modified the velveth, velvetg and oases versions for Galaxy so as to include input for directory name (where the readable data can be stored). Now, when I extracted the workflow, I found that the directory path cannot be replaced. Is there a way that I could override this? Cheers, CL

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Files not ending in .dat
by Ciara Ledero 21 May '12

21 May '12

Hi all, While I was checking Galaxy's database folder, I noticed that some of the files there did not end in .dat. For example, I had dataset_150.dat.bam, dataset_194.dat.fai and dataset_442_files. Can they be removed via the delete and purge scripts of Galaxy? Cheers, CL

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Re: [galaxy-dev] ERROR on History export
by Todd Oakley 20 May '12

20 May '12

Hi Jeremy, I am no longer getting the same Error when exporting a history. However, I've now encountered a new problem. Namely, I am never able to actually download the file that Galaxy tells me it produced. I never can get past the web page that says: Exporting History 'name of history here'. Use this link to download the archive or import it to another Galaxy server: <http://knot.cnsi.ucsb.edu:8080/history/export_archive?id=9c1d880a9fc5e123><link to history here> I thought at first perhaps this was just taking time, but after a few hours, I still got the same. Also, I tested a very simple history with 1 tiny file, and got the same result. I'm using Firefox, and our Galaxy instance uses only Galaxy as the web server, no Apache or nginx Thanks again for any advice! Todd On 4/26/2012 10:35 AM, Jeremy Goecks wrote: > I reproduced myself, diagnosed the issue, and committed a fix to > -central. Once you update your Galaxy (or you update to the next > distribution when it becomes available), the export should work. > > Best, > J. > > On Apr 26, 2012, at 12:49 PM, Todd Oakley wrote: > >> Sorry, I don't use the main Galaxy instance, I imagine I won't be >> able to reproduce the bug there anyway. Most of the tools I use are >> in-house for phylogenetics (we'll put them up on the tool shed in the >> next few weeks). I can ask a postdoc in my lab to try to export some >> histories, as he uses the main instance. >> >> We can try to debug here. Can you point to a place to start looking >> (I haven't looked at the Galaxy code at all beyond universe.ini and >> tools)? >> >> Thanks, >> >> Todd >> >> On 4/26/2012 5:41 AM, Jeremy Goecks wrote: >>> Hi Todd, >>> >>> History export is a beta feature and hasn't been fully tested yet. >>> We'll look into this, but it's difficult to diagnose a bug on a >>> local instance. Can you reproduce on either our main or test server? >>> >>> Thanks, >>> J. >>> >>> On Apr 25, 2012, at 8:08 PM, Todd Oakley wrote: >>> >>>> Hello, >>>> I'd am trying to export histories to upload to another galaxy >>>> instance. >>>> >>>> For some histories, it works fine. However, for others, I get >>>> an error. When I turn on debug, I get the error pasted below. Any >>>> thoughts on what is the cause of "object has no attribute 'hid'"? >>>> >>>> Thanks! >>>> Todd >>>> >>>> >>>> >>>> Server Error >>>> >>>> Module paste.exceptions.errormiddleware:*143* in |__call__| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>app_iter >>>> *=* self*.*application*(*environ*,* start_response*)*| >>>> Module paste.debug.prints:*98* in |__call__| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>environ*,* >>>> self*.*app*)*| >>>> Module paste.wsgilib:*539* in |intercept_output| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>app_iter >>>> *=* application*(*environ*,* replacement_start_response*)*| >>>> Module paste.recursive:*80* in |__call__| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* >>>> self*.*application*(*environ*,* start_response*)*| >>>> Module paste.httpexceptions:*632* in |__call__| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* >>>> self*.*application*(*environ*,* start_response*)*| >>>> Module galaxy.web.framework.base:*145* in |__call__| >>>> |>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>body >>>> *=* method*(* trans*,* ****kwargs *)*| >>>> Module galaxy.web.controllers.history:*591* in |export_archive| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>history_exp_tool*.*execute*(* >>>> trans*,* incoming *=* params*,* set_output_hid *=* True *)*| >>>> Module galaxy.tools:*1276* in |execute| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>*return* >>>> self*.*tool_action*.*execute*(* self*,* trans*,* >>>> incoming*=*incoming*,* set_output_hid*=*set_output_hid*,* >>>> history*=*history*,* ****kwargs *)*| >>>> Module galaxy.tools.actions.history_imp_exp:*103* in |execute| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>include_deleted*=*incoming*[* >>>> 'include_deleted' *]* *)*| >>>> Module galaxy.tools.imp_exp:*419* in |setup_job| >>>> |>> >>>> <http://knot.cnsi.ucsb.edu:8080/history/export_archive#>input_datasets >>>> *=* *[* assoc*.*dataset*.*hid *for* assoc *in* job*.*input_datasets >>>> *]*| >>>> *AttributeError: 'NoneType' object has no attribute 'hid'* >>>> -- >>>> >>>> *************************************** >>>> Todd Oakley, Professor >>>> Ecology Evolution and Marine Biology >>>> University of California, Santa Barbara >>>> Santa Barbara, CA 93106 USA >>>> *************************************** >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> >>>> http://lists.bx.psu.edu/ >>> >>> >>> >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> >>> http://lists.bx.psu.edu/ >> >> -- >> >> *************************************** >> Todd Oakley, Professor >> Ecology Evolution and Marine Biology >> University of California, Santa Barbara >> Santa Barbara, CA 93106 USA >> *************************************** >> >> Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/> >> Twitter: @UCSB_OakleyLab >> >> *Recent Papers: * >> >> * Cnidocyte discharge regulated by opsin and light >> BMC Biology Paper <http://tinyurl.com/7dajl2q> | Scientific >> American Write-up >> <http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-wh…> >> >> * Sponge Larvae Could be Guided by Cryptochrome >> J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> | >> Nature News >> <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html> >> > -- *************************************** Todd Oakley, Professor Ecology Evolution and Marine Biology University of California, Santa Barbara Santa Barbara, CA 93106 USA *************************************** Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/> Twitter: @UCSB_OakleyLab *Recent Papers: * * Cnidocyte discharge regulated by opsin and light BMC Biology Paper <http://tinyurl.com/7dajl2q> | Scientific American Write-up <http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-wh…> * Sponge Larvae Could be Guided by Cryptochrome J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> | Nature News <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html>

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A tool to export only history details
by Jean-Francois Payotte 18 May '12

18 May '12

Hi, I am new to galaxy but I've been asked to implement some kind of tool which would automatically export the history details (the information we can find when hitting the 'view details' button) to a file, for an entire workflow. Let's say we run some analyses using some workflow, the basic idea (if that is possible) would be to insert the new tool at the end of the workflow, specifying an output directory, and this new tool would extract only history details and would save it to a file in the specified directory. Right now, I have no idea if that's even possible, and if it is, I am not sure where to start. I tried searching the mailing-list archive.. but I couldn't find answers to my problem. So if someone could point me in any direction to help me achieve this kind of tool, that would be greatly appreciated. Best regards, Jean-François

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